more often than not, i have to save what i am working on extremely frequently, as Eagle seems to just up and die (stops responding, and shuts down). i have just now updated to 3.6.3, so maybe that particular bug is now fixed.
unfortunately, my last schematic i was working on when it died, is corrupted and can't be read. so sadly, i have to re-draw it from scratch.
I don't use Eagle so i don't know that trouble.
But these things happen.
So i just save projects with addition of a version number to the filename whenever i made a change.
Version numbers change different, depending how large the change was.
This might get you a lot of files to handle, but it will prevent the total loss of all work like you just experienced.
And also, if a major change wasn't what you had in mind, you just need to go a few files back and branch in a different direction from there.
Of course you can also make backups of all files you're working on, in shorter intervals.